Am sorry Dr. Case. It was a typo mistake.
complex: *Protein + ligand + cofactor *
receptor: *Protein + cofactor*
ligand: *ligand*
Does the order of the components are really important. Bcoz only in this
case am facing problem. If the ligand placed at the end of the PDb
coordinate files, its not giving any error.
On Tue, Feb 19, 2019 at 10:47 PM M RCC <mkr3j2c1.gmail.com> wrote:
> Dear Amber Users,
> I am facing an error in PBSA calculation. and I need a few clarifications.
>
> My system contains the coordinates of following in the specified order.
> Protein + ligand + cofactor
> MD simulation running well without any error.
> While performing MMPBSA calculation I have prepared the topology as follows
> complex: *Protein + ligand + cofactor *
> receptor: *Protein + ligand + cofactor*
> ligand: *ligand*
>
> While starting the calculation it gives an error with the complex
> topology. I checked the mdout files. It says NATOM mismatch error. I have
> comverted the prepared topology & crd files of complex and receptor to PBD
> files and it shows the equal number of atoms.
>
> What am possibly missing here?
> Does it bcoz of the order of the protein and ligand coordinates?
>
>
>
>
>
>
>
>
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Received on Wed Feb 20 2019 - 04:00:01 PST
